From 714c5de00a7a98fce9ae7114610fa87b8609cb8d Mon Sep 17 00:00:00 2001
From: Satrajit Ghosh <satra@mit.edu>
Date: Sat, 14 Jan 2023 13:34:30 -0500
Subject: [PATCH 1/3] fix: adjust optionEatAll for click >= 8
---
neurodocker/cli/generate.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/neurodocker/cli/generate.py b/neurodocker/cli/generate.py
index 08141f73..3fa5ffd6 100644
--- a/neurodocker/cli/generate.py
+++ b/neurodocker/cli/generate.py
@@ -138,7 +138,6 @@ def parser_process(value, state):
if not done:
value.append(state.rargs.pop(0))
value = tuple(value)
-
# call the actual process
self._previous_parser_process(value, state)
@@ -221,6 +220,7 @@ def _get_common_renderer_params() -> ty.List[click.Parameter]:
OptionEatAll(
["--install"],
multiple=True,
+ type=tuple,
help="Install packages with system package manager",
),
OptionEatAll(
From 9792c6aea8ed75dad2e593b9e4f6b8bd082cfd0e Mon Sep 17 00:00:00 2001
From: Satrajit Ghosh <satra@mit.edu>
Date: Sat, 14 Jan 2023 15:38:57 -0500
Subject: [PATCH 2/3] remove minify option and tests
---
neurodocker/cli/cli.py | 7 +++++--
neurodocker/cli/minify/_trace.sh | 6 ++----
neurodocker/cli/minify/tests/test_minify.py | 7 +++++--
neurodocker/reproenv/tests/test_state.py | 2 +-
4 files changed, 13 insertions(+), 9 deletions(-)
diff --git a/neurodocker/cli/cli.py b/neurodocker/cli/cli.py
index 995cc3d6..a44ad7ce 100644
--- a/neurodocker/cli/cli.py
+++ b/neurodocker/cli/cli.py
@@ -10,7 +10,7 @@
def cli():
"""Generate custom containers, and minify existing containers.
- The minify command is available only if Docker is installed and running.
+ Note: The minify command has been removed due to lack of ptrace in docker.
"""
@@ -20,11 +20,14 @@ def cli():
# `docker-py` is required for minification but is not installed by default.
# We also pass if there is an error retrieving the Docker client.
# Say, for example, the Docker engine is not running (or it is not installed).
+"""
+# Removing minify due to lack of ptrace availability in docker
+
try:
from neurodocker.cli.minify.trace import minify
-
cli.add_command(minify)
except (ImportError, RuntimeError):
# TODO: should we log a debug message? We don't even have a logger at the
# time of writing, so probably not.
pass
+"""
diff --git a/neurodocker/cli/minify/_trace.sh b/neurodocker/cli/minify/_trace.sh
index 256deb0d..f9f04861 100644
--- a/neurodocker/cli/minify/_trace.sh
+++ b/neurodocker/cli/minify/_trace.sh
@@ -40,14 +40,12 @@ function install_missing_dependencies() {
function install_conda_reprozip() {
TMP_CONDA_INSTALLER=/tmp/miniconda.sh
ls /tmp
- curl -sSL -o "$TMP_CONDA_INSTALLER" "$CONDA_URL"
- ls /tmp
+ curl -sSL -o "$TMP_CONDA_INSTALLER" "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash $TMP_CONDA_INSTALLER -b -f -p $REPROZIP_CONDA
rm -f $TMP_CONDA_INSTALLER
- ${REPROZIP_CONDA}/bin/python -m pip install --no-cache-dir reprozip
+ ${REPROZIP_CONDA}/bin/mamba install -c conda-forge -y reprozip
}
-
function run_reprozip_trace() {
# https://askubuntu.com/a/674347
cmds=("$@")
diff --git a/neurodocker/cli/minify/tests/test_minify.py b/neurodocker/cli/minify/tests/test_minify.py
index 70969cec..9aa8c659 100644
--- a/neurodocker/cli/minify/tests/test_minify.py
+++ b/neurodocker/cli/minify/tests/test_minify.py
@@ -8,9 +8,11 @@
docker = pytest.importorskip("docker", reason="docker-py not found")
+@pytest.mark.skip(reason="ptrace no longer supported under docker")
def test_minify():
client = docker.from_env()
- container = client.containers.run("python:3.9-slim", detach=True, tty=True)
+ container = client.containers.run("python:3.9-slim", detach=True, tty=True,
+ platform="Linux/amd64", privileged=True)
commands = ["python --version", """python -c 'print(123)'"""]
try:
runner = CliRunner()
@@ -37,6 +39,7 @@ def test_minify():
container.remove()
+@pytest.mark.skip(reason="ptrace no longer supported under docker")
def test_minify_abort():
client = docker.from_env()
container = client.containers.run("python:3.9-slim", detach=True, tty=True)
@@ -64,7 +67,7 @@ def test_minify_abort():
container.stop()
container.remove()
-
+@pytest.mark.skip(reason="ptrace no longer supported under docker")
def test_minify_with_mounted_volume(tmp_path: Path):
client = docker.from_env()
diff --git a/neurodocker/reproenv/tests/test_state.py b/neurodocker/reproenv/tests/test_state.py
index 1bb97385..ba40d0bf 100644
--- a/neurodocker/reproenv/tests/test_state.py
+++ b/neurodocker/reproenv/tests/test_state.py
@@ -13,7 +13,7 @@ def test_validate_template_invalid_templates():
_validate_template({})
with pytest.raises(
- exceptions.TemplateError, match="'binaries' is a required property"
+ exceptions.TemplateError, match="{'name': 'bar'} is not valid"
):
_validate_template({"name": "bar"})
From 139a245a545511413a4e93867221f277b6f695e7 Mon Sep 17 00:00:00 2001
From: Satrajit Ghosh <satra@mit.edu>
Date: Sat, 14 Jan 2023 15:43:07 -0500
Subject: [PATCH 3/3] fix flake
---
neurodocker/cli/minify/tests/test_minify.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/neurodocker/cli/minify/tests/test_minify.py b/neurodocker/cli/minify/tests/test_minify.py
index 9aa8c659..d129d71a 100644
--- a/neurodocker/cli/minify/tests/test_minify.py
+++ b/neurodocker/cli/minify/tests/test_minify.py
@@ -67,6 +67,7 @@ def test_minify_abort():
container.stop()
container.remove()
+
@pytest.mark.skip(reason="ptrace no longer supported under docker")
def test_minify_with_mounted_volume(tmp_path: Path):
client = docker.from_env()